The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA requires extensive algorithmic support, considering the size of the genomes that have been sequenced or are still in the pipeline. GenAlyzer was implemented based on enhanced suffix arrays, providing an efficient and complete detection of various types of repeats (e.g. direct or forward, exact or degenerate) together with an evaluation of significance and an interactive visualization. Working in close collaboration with biologists, GenAlyzer was applied in different areas of sequence analysis: checking fragment assemblies, searching for low copy repeats, finding unique sequences, comparing gene structures, mapping of cDNA or EST sequences. Finally, it was also possible to improve the tool to handle also inter-genomic repeat analysis, i.e, whole genome comparisons. Besides the wide scope of biological applications provided by GenAlyzer, another great advantage is the user-friendly visualization. While other software tools often produce only static views, GenAlyzer is fully interactive. The user can zoom into or out of regions of interest, getting any kind of information about a special repeat, like position, direction, significance or even the sequence itself. During the zooming process, an overview window keeps showing the entire computed repeat pattern, highlighting the zoomed region in a red framed box. This avoids the user to loose its orientation in the analysed sequence.
Overall, the manifold applications of GenAlyzer has shown that the tool is used for many other sequence analysis tasks than it was originally thought for, considering the many ways of interpreting biological repeats.
Currently, GenAlyzer is being used in several german as well as international genome analysis projects, resulting in a fundamental tool for initial genomic scale studies.

Jomuna V. ChoudhuriStefan KurtzRobert GiegerichJens Stoye, Chris Schleiermacher, Enno Ohlebusch


3 years

German Research Foundation - DFG, GK Bioinformatik 635

Fri Dec 19 10:54:56 CET 2014